Affiliation: Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

ABSTRACTWe performed a Phenome-wide association study (PheWAS) utilizing diverse genotypic and phenotypic data existing across multiple populations in the National Health and Nutrition Examination Surveys (NHANES), conducted by the Centers for Disease Control and Prevention (CDC), and accessed by the Epidemiological Architecture for Genes Linked to Environment (EAGLE) study. We calculated comprehensive tests of association in Genetic NHANES using 80 SNPs and 1,008 phenotypes (grouped into 184 phenotype classes), stratified by race-ethnicity. Genetic NHANES includes three surveys (NHANES III, 1999-2000, and 2001-2002) and three race-ethnicities: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We identified 69 PheWAS associations replicating across surveys for the same SNP, phenotype-class, direction of effect, and race-ethnicity at p<0.01, allele frequency >0.01, and sample size >200. Of these 69 PheWAS associations, 39 replicated previously reported SNP-phenotype associations, 9 were related to previously reported associations, and 21 were novel associations. Fourteen results had the same direction of effect across more than one race-ethnicity: one result was novel, 11 replicated previously reported associations, and two were related to previously reported results. Thirteen SNPs showed evidence of pleiotropy. We further explored results with gene-based biological networks, contrasting the direction of effect for pleiotropic associations across phenotypes. One PheWAS result was ABCG2 missense SNP rs2231142, associated with uric acid levels in both non-Hispanic whites and Mexican Americans, protoporphyrin levels in non-Hispanic whites and Mexican Americans, and blood pressure levels in Mexican Americans. Another example was SNP rs1800588 near LIPC, significantly associated with the novel phenotypes of folate levels (Mexican Americans), vitamin E levels (non-Hispanic whites) and triglyceride levels (non-Hispanic whites), and replication for cholesterol levels. The results of this PheWAS show the utility of this approach for exposing more of the complex genetic architecture underlying multiple traits, through generating novel hypotheses for future research.

pgen-1004678-g007: Sun plot of (p<0.01) results for LIPC rs1800588, coded allele T.This SNP was previously associated HDL-C in European-descent populations. Significant associations (p<0.01) are plotted clockwise with the most significant value result at the top. The length of the each line corresponds to the –log(p-value) of each result, with the longest line representing the most significant result for this SNP, meeting our PheWAS replication criteria for inclusion. Study, transformed (LN +1) or untransformed (none) phenotype description, self-reported race-ethnicity, and direction of effect are listed for each association. This SNP was associated with a number of phenotypes including folate in Mexican Americans (MA), total cholesterol in non-Hispanic whites (NHW), triglyceride levels in non-Hispanic whites, and vitamin E levels in non-Hispanic whites.

Mentions:
For another example, rs2338104, an intronic SNP in KCTD10, which was previously associated with HDL cholesterol (HDL-C) in European-descent populations [17], [25], was associated here with hemoglobin and hearing levels, both novel results in non-Hispanic whites (Fig. 6). Another example of potential pleiotropy was for SNP rs1800588 near LIPC, previously associated HDL-C in European-descent populations [15]. We observed significant associations between this SNP and the novel phenotypes of folate (in Mexican Americans) and vitamin E levels (in non-Hispanic whites), as well as replication for cholesterol and the related phenotype of triglycerides (both in non-Hispanic whites; Fig. 7). The intronic SNP rs174547 of FADS1 provides another example. This SNP was previously associated with phospholipid levels [39], resting heart rate [40], phosphatidylcholine levels [41], HDL-C and triglyceride levels [17] in individuals of European ancestry. Here, this SNP is associated with ferritin levels in Mexican Americans and with folate levels in non-Hispanic blacks.

pgen-1004678-g007: Sun plot of (p<0.01) results for LIPC rs1800588, coded allele T.This SNP was previously associated HDL-C in European-descent populations. Significant associations (p<0.01) are plotted clockwise with the most significant value result at the top. The length of the each line corresponds to the –log(p-value) of each result, with the longest line representing the most significant result for this SNP, meeting our PheWAS replication criteria for inclusion. Study, transformed (LN +1) or untransformed (none) phenotype description, self-reported race-ethnicity, and direction of effect are listed for each association. This SNP was associated with a number of phenotypes including folate in Mexican Americans (MA), total cholesterol in non-Hispanic whites (NHW), triglyceride levels in non-Hispanic whites, and vitamin E levels in non-Hispanic whites.

Mentions:
For another example, rs2338104, an intronic SNP in KCTD10, which was previously associated with HDL cholesterol (HDL-C) in European-descent populations [17], [25], was associated here with hemoglobin and hearing levels, both novel results in non-Hispanic whites (Fig. 6). Another example of potential pleiotropy was for SNP rs1800588 near LIPC, previously associated HDL-C in European-descent populations [15]. We observed significant associations between this SNP and the novel phenotypes of folate (in Mexican Americans) and vitamin E levels (in non-Hispanic whites), as well as replication for cholesterol and the related phenotype of triglycerides (both in non-Hispanic whites; Fig. 7). The intronic SNP rs174547 of FADS1 provides another example. This SNP was previously associated with phospholipid levels [39], resting heart rate [40], phosphatidylcholine levels [41], HDL-C and triglyceride levels [17] in individuals of European ancestry. Here, this SNP is associated with ferritin levels in Mexican Americans and with folate levels in non-Hispanic blacks.

Affiliation:
Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America.

ABSTRACTWe performed a Phenome-wide association study (PheWAS) utilizing diverse genotypic and phenotypic data existing across multiple populations in the National Health and Nutrition Examination Surveys (NHANES), conducted by the Centers for Disease Control and Prevention (CDC), and accessed by the Epidemiological Architecture for Genes Linked to Environment (EAGLE) study. We calculated comprehensive tests of association in Genetic NHANES using 80 SNPs and 1,008 phenotypes (grouped into 184 phenotype classes), stratified by race-ethnicity. Genetic NHANES includes three surveys (NHANES III, 1999-2000, and 2001-2002) and three race-ethnicities: non-Hispanic whites (n = 6,634), non-Hispanic blacks (n = 3,458), and Mexican Americans (n = 3,950). We identified 69 PheWAS associations replicating across surveys for the same SNP, phenotype-class, direction of effect, and race-ethnicity at p<0.01, allele frequency >0.01, and sample size >200. Of these 69 PheWAS associations, 39 replicated previously reported SNP-phenotype associations, 9 were related to previously reported associations, and 21 were novel associations. Fourteen results had the same direction of effect across more than one race-ethnicity: one result was novel, 11 replicated previously reported associations, and two were related to previously reported results. Thirteen SNPs showed evidence of pleiotropy. We further explored results with gene-based biological networks, contrasting the direction of effect for pleiotropic associations across phenotypes. One PheWAS result was ABCG2 missense SNP rs2231142, associated with uric acid levels in both non-Hispanic whites and Mexican Americans, protoporphyrin levels in non-Hispanic whites and Mexican Americans, and blood pressure levels in Mexican Americans. Another example was SNP rs1800588 near LIPC, significantly associated with the novel phenotypes of folate levels (Mexican Americans), vitamin E levels (non-Hispanic whites) and triglyceride levels (non-Hispanic whites), and replication for cholesterol levels. The results of this PheWAS show the utility of this approach for exposing more of the complex genetic architecture underlying multiple traits, through generating novel hypotheses for future research.